The issue is exactly as described in https://answers.atlassian.com/questions/73889/greenhopper-s-rapid-board-are-empty-after-upgrading-to-5-10-6
Seems that the answer there is also correct because after some of the developers updated some of their tasks/bugs these started to appear in the rapid board.
I also have a query: project = SCRUM AND sprint in openSprints() and status in (In Progress, Open, Reopened) ORDER BY Rank ASC, key ASC which initially failed telling me there is no open sprints and now one recently changed task appears in it.
I removed the recently used quick filter from the rapid board because we never used it and needed the space for our own quick filters.